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| Status |
Public on Jul 17, 2018 |
| Title |
n2_wildtypexxx_sy002 |
| Sample type |
SRA |
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| Source name |
Bristol N2
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain background: N2
genotype/variation: Bristol N2
developmental stage: mixed stage
tissue: whole worm
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| Treatment protocol |
Worms were harvested from the plates by washing them off with M9 media
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| Growth protocol |
Indicated strains were grown at 20C on NGM agar plates fed OP50 E. coli
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Worms were lysed in Trizol and total RNA recovered according to manufacturers protocol.
mRNA libraries for high throughput sequencing were prepared from polyA selected mRNAs extracted from 5µg of total RNA using the NEXTflex Rapid Directional qRNA-Seq Kit (BioO Scientific). 8bp at the 5' ends of both read1 and read2 constitute a molecular index. Paired directional 101nt or 100nt reads, 8 libraries per lane, were obtained from an Illumina HiSeq 4000 operated by the QB3 Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
N2-4
n2_wildtypexxx_sy002
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| Data processing |
10bp were trimmed from the 5' end of read1 and read2 (including 8bp of molecular index). 11bp (length 101 reads) or 10bp (length 100 reads) were trimmed from the 3' end of read1 and read2 leaving 80bp for read1 and 80bp for read2 for each sample.
Trimmed reads were mapped with Bowtie2 to the RepeatMasker library of C.elegans repeat elements.
After removing reads with both ends mapped to repeat elements, the remaining trimmed reads were mapped to the indicated genome assembly using STAR.
Potential PCR duplicates within each set of reads having a common molecular index were removed with samtools rmdup.
Splice junctions were extracted from the bam files by examining the CIGAR string, resulting in a non-redundant set of introns spanned by these splice junctions.
Alternative splicing events were identified from the splice junctions.
A5SS events: A custom script was employed to identify junctions that define alternative 5' ss separated by <50bp across the libraries mapped to the indicated genome assembly.
A3SS events: A custom script was employed to identify junctions that define alternative 3' ss separated by <50bp across the libraries mapped to the indicated genome assembly.
SE events: AltEventFinder (Zhou A et al. 2012) was used to identify alternative cassette exons in the wormBase genes for each genome assembly.
MISO was run on each sample to determine PSI (percent spliced in) for A5SS, A3SS, and SE events from the indicated genome assembly.
The MISO results for a sample were merged into a gtf with the scores for the 2 transcripts of an event representing its PSI value.
Genome_build: May 2008 (WS190/ce6) for samples *_mrNNN. Oct. 2010 (WS220/ce10) for samples *_syNNN.
Supplementary_files_format_and_content: For each sample, a gtf file, including a UCSC genome browser track line, of A5SS, A3SS, SE events, where the score field for a transcript represents PSI for that event in this sample.
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| Submission date |
Apr 17, 2018 |
| Last update date |
Jul 18, 2018 |
| Contact name |
Alan M Zahler |
| E-mail(s) |
zahler@ucsc.edu
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| Phone |
8314595131
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| Organization name |
UC Santa Cruz
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| Department |
MCD Biology
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| Lab |
Zahler Lab
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| Street address |
Sinsheimer Labs
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| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
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| Platform ID |
GPL22765 |
| Series (1) |
| GSE113275 |
Global alternative splicing analysis of cryptic splicing suppressors in C. elegans |
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| Relations |
| BioSample |
SAMN08942873 |
| SRA |
SRX3948158 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3101971_n2_wildtypexxx_sy002.miso.merged.events.ce10.gtf.track.gz |
393.7 Kb |
(ftp)(http) |
TRACK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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